From: s.bora erdemli (serdemli_at_ku.edu.tr)
Date: Wed Jul 20 2005 - 21:06:53 CDT
Hi;
I think the script is in page 45 in the NAMD tutorial, but just in case I
copied and pasted ....
you can do it with the following tcl script and using VMD:
mol load psf myprotein-water.psf dcd myprotein-water.dcd ----->
load your psf and corresponding dcd file
set nf [molinfo top get numframes]
for {set i 0 } {$i < $nf } {incr i } {
set sel [atomselect top protein frame $i] ------>
select whatever part you want to extract from pdb in your case the protein
$sel writepdb $i.pdb
}
mol load psf myprotein-prot.psf -------> you
need to have also .psf file of your protein without water
for {set i 0 } {$i < $nf } {incr i } {
animate read pdb $i.pdb }
animate write dcd {myprotein-prot.dcd} waitfor all top ----->
this line creates .dcd file without water in your case
for {set i 0 } {$i < $nf } {incr i } {
puts "Removing file $i.pdb"
}
exit
best regards
Sabri Bora Erdemli
Research and Teaching Asistant
KOC UNIVERSITY
Computational Sciences and Engineering
Istanbul/Turkey
----- Original Message -----
From: "Stern, Julie" <jvstern_at_bnl.gov>
To: <namd-l_at_ks.uiuc.edu>
Sent: Thursday, July 21, 2005 3:49 AM
Subject: namd-l: removing water from DCD
> Hello,
> What is the best way to remove water
> from the DCD file after it has been created?
> Are there any postprocessing tools for this?
>
> Thanks.
>
> --Julie
>
>
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